Getting nearer now!
Holes: ones already done, no worry about them, any more than in any house.
Holes to be made come into these categories:
tiny ones for small pictures should be OK on the internal wall material.
small ones to take weight (such as for shelves) must be made in to the timber because the insulating material will not take the weight. There should be plans showing where the timbers run - if not then whoever is putting them up has to knock on the walls to guess and then make a 'test hole'.
You can't knock down timbers to make large holes in walls because of weakening the structure.
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I don't know why your friend told you that you mustn't breach the insulating material - it must be to do with the insulating stuff itself in their house. Can the surveyor tell you what was used (then you can google it)? Most timber frame houses have 'soft' insulation that you can stuff in all the gaps (ah yes, I remember it well!)
No more damp penetrates than in an ordinary house. Are you worried about the wood getting damp? It is treated against rot and damp, but as I've said, any damp shouldn't come anywhere near the wood anyway as all the pipework passes through the gaps in the frame.
The house should have some sort of warranty - although they only last for about 10 years these days, it is an indicator that it was built to correct standards. Legally it should be - I presume you have asked the surveyor? So that you know how it works, the local authority building inspector comes out to inspect at every significant stage of a self-build house - the builders submit these certificates to one of the major warranty companies. We used LABC www.labcwarranty.co.uk/ but they all work the same way.
Whatever else, the local building inspector must have signed off that it was a sound building.
So, in my opinion, you need to ask the surveyor again about its integrity as a building (nothing to do with the timber frame)
Do you know if they used a timber frame company, or designed the frame themselves? I would look up the company, but if you want a general idea about how timber frame houses / self -build works, this is one of the biggest companies: www.potton.co.uk/design-build/pricing-structure-build-cost-guide
this may also help: www.homebuilding.co.uk/